A wide variety of techniques that include placing a sample on a substrate have been developed to prepare and analyze biological samples. Examples of such techniques include microscopy, micro-array analyses (such as protein and nucleic acid micro-array analyses) and mass spectrometric methods such as MALDI and SELDI. In each of these techniques, preparation of samples for analysis can include contacting the sample on the substrate with one or more liquids. Where a sample is treated with multiple liquids, both application and subsequent removal of liquids can be important for providing a sample suitable for analysis.
In the context of microscope slides bearing biological samples (such as tissue sections or cells), the sample is typically treated with one or more dyes or conjugates of specific binding agents with detectable labels (such as nucleic acid probes and antibodies labeled with enzymes or fluorescent moieties) to add color and contrast to otherwise transparent or invisible cells or cell components. Historically, preparation of samples on microscope slides for analysis has included manual immersion of slides in containers of reagents. This labor intensive process suffers from a variety of shortcomings including inconsistency and carryover of reagents between containers, which leads to contamination and degradation of reagents.
Automation of the slide preparation process has helped to overcome the inherent inconsistency of the manual process, but many automated slide staining instruments simply try to replicate the manual process (see, for example, U.S. Pat. No. 6,017,495). While such “dip and dunk” type staining instruments increase throughput and consistency, they are not suited for more advanced staining protocols such as immunohistochemical (IHC) staining and in situ hybridization (ISH), especially because they do not eliminate reagent carryover between containers and generally do not provide adequate control over temperature.
Automated staining systems have been devised that are capable of advanced staining protocols such as IHC and ISH. Many of these systems apply liquids to a sample held on the top surface of a slide, and the liquid is either allowed to puddle over the sample (see, for example, U.S. Pat. No. 6,827,901) or is contained within a removable chamber that covers the top of the slide (see, for example, U.S. Pat. No. 6,218,191). Since IHC and ISH analyses are particularly sensitive to residual reagents left behind on a sample, these systems utilize repeated washing steps to remove residual reagents from the sample. Washing generates additional laboratory waste, adds expense to slide preparation and reduces throughput.
Another approach to applying liquids to substrates is illustrated by the platen-based systems described, for example, in U.S. Pat. Nos. 3,431,886, 4,200,056 and 5,700,346. These systems have found application in performing simple primary staining protocols such as hematoxylin and eosin (H&E) staining and Wright staining where significant residual reagent volumes left on a microscope slide between individual protocol steps can be tolerated. However, such systems were not designed for and do not appear capable of removing residual reagent volumes to an extent that permits more sophisticated staining protocols such as IHC and ISH. Furthermore, such systems do not incorporate a means for temperature control that is important for implementing advanced IHC and ISH protocols.
What is needed is an automated system that more effectively manages the application, and especially removal, of reagents from biological samples placed on substrates. Furthermore, a system that segregates different liquid wastes from multiple steps in a sample treatment process would be advantageous. A system that is configurable, flexible and can be easily adapted to perform multiple sample treatment protocols (such as primary and special staining protocols, IHC and ISH) also is desirable.